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Allowing cysteines to repack

Hello all, I am working on using PyRosetta to improve a homology-derived protein structure, in which the disulfide bonds are not in their ideal configuration. After playing around with the refinement.py script in the tutorials, I noticed that it was leaving the disulfides untouched in the output results. I noticed in the manual (under TaskFactory) that PyRosetta/Rosetta disables cysteine repacking by default. It wasn't clear to me how to disable this behavior. I tried the following after initializing the packmover:

rr = RestrictResidueToRepacking()
rr.include_residue( 4 )

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how to reconstruct the whole complex after symmetric docking

symmetric docking uses the minimal subsystem during docking. The output contains also the smallest subsystem. For example, in a C17 system (3kml), only three neighboring subunits are used in docking and the output decoys contain also only three subunits (DiMaio2011, PLoS ONE). How to reconstruct the complete system based on the output? It seems the original symmetric definition file can not be relied on any more.

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Any info on 1) building for CUDA and 2) with the PGI compiler suite

In looking to try out a build of Rosetta so that a researcher in another
department can try it out on a large memory resource we have here, I
noticed, because I ended up looking at this file, that there's a stanza
in

tools/build/basic.settings

that appears to allow for compilation against a CUDA toolkit.

As I am not a Rosetta user but an implementer, I was wondering if there's
a simple test/demo that I could try out, if I build such a variant, which
would be an Ubuntu 10.10 (GCC 445) with NVIDIA_GPU_Computing_SDK-4.0.

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Need help with compilation (How to test if compilation is sucessful)

I logged in as a regular user without superuser privilege.
After I downloaded rosetta 3.4, and unzipped the file "rosetta3.4_bundles.tgz", I unzipped all the .tgz files in the directory "rosetta3.4". In the sub-directory "rosetta_source", I typed "python external/scons-local/scons.py bin mode=release". After some time (hours), the compilation seems completed. then in the directory rosetta3.4/rosetta_source/bin, I typed "minirosetta.linuxgccrelease", get the following error message:

core.init: Mini-Rosetta version unknown from unknown
core.init: command: minirosetta.linuxgccrelease

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"No SConstruct file found" when install rosetta 3.4 on ubuntu 11.10

According to the instruction, I first installed scons and tested it, it seems working:

*********************
~/scons-2.1.0$ scons --version
SCons by Steven Knight et al.:
script: v2.1.0.r5357[MODIFIED], 2011/09/09 21:31:03, by bdeegan
on ubuntu
engine: v2.1.0.r5357[MODIFIED], 2011/09/09 21:31:03, by bdeegan
on ubuntu
engine path: ['/usr/local/lib/scons-2.1.0/SCons']
Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009,
2010,
2011 The SCons Foundation
**************************

Then I run Resetta installation and get error below:

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The design of a helical peptide

Dear Rosetta developers,

I am interested in the de novol design of a peptide with helical conformation which could bind a specific protein partner with enhanced affinity. However, when consulting the user guide, i lost my way about the specific method. So could you be so kindly to tell me which method or module in Rosetta can do such kind of case , or provide me a step-by-step guidance.

What i intended to do was listed in the following:

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